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year-2000

Publications during 2000

Article Reference A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations
 
Article Reference A Density Functional Theory Study of a Silica-Supported Zirconium Monohydride Catalyst for Depolymerization of Polyethylene
A silica-supported zirconium hydride catalyst for depolymerization of polyethylene is studied using density functional theory (DFT) together with a generalized gradient approximation (GGA) for the exchange and correlation energy. The (100) and (111) surfaces of beta-cristobalite are used as two possible models of a silica surface. Based on the experimental surface structure determined by J. Corker et al. (Science 1996, 271, 966), we propose a detailed atomic model of the zirconium monohydride that is believed to be the active site for depolymerization of polyolefins. Our model of the zirconium monohydride on the (100) surface is found to be very stable and the structure is in good agreement with extended X-ray absorption fine structure (EXAFS) measurements. We have carried out depolymerization of a small polyolefin chain (C3H8) to give CH4 and C2H6 by addition of H2. The rate-limiting step is a beta-methyl transfer to the zirconium atom, and the activation energy is 29 kcal/mol on the (100) surface.
Article Reference Ab initio analysis of proton transfer dynamics in (H2O)3H+
We have harvested ab initio trajectories of proton transfer in (H2O)3H+ by combining Car-Parrinello molecular dynamics (CPMD) with the transition path sampling method. Two transition state regions contribute to these dynamics, with saddle points similar to those identified by Geissler, Dellago, and Chandler for an empirical model of the same cluster [Phys. Chem. Chem. Phys. 1 (1999) 1317]. As in that model, the location of a transition state along a finite-temperature trajectory indicates that proton transfer is driven by reorganization of the oxygen ring. From vibrational properties it is estimated that the characteristic time for proton transfer is ˊ1 ns at a temperature of 300 K.
Article Reference Ab initio molecular dynamics simulation of methanol interacting with acidic zeolites of different framework structure
Ab initio molecular dynamics simulations based on density-functional theory together with a plane-wave basis set are performed on the adsorption of a single methanol molecule in the series of acidic zeolites theta-1, ferrierite and ZSM-5. We only find a physisorbed molecule as a stable structure. Comparison is made with previous calculations on methanol in chabazite which used the same techniques. The calculated adsorption energies are -131 (theta-1/O2), -128 (theta-1/O4), -121 (ferrierite) and -139 (ZSM-5) kJ mol-1. The deprotonation energies are 1241 (ZSM-5), 1244 (ferrierite), 1261 (theta-1/O4) and 1262 (theta-1/O2) kJ mol-1. The adsorption energies as well as the deprotonation energies show differences of only 20 kJ mol-1.
Article Reference Ab initio molecular dynamics studies on HIV-1 reverse transcriptase triphosphate binding site: Implications for nucleoside-analog drug resistance
 
Article Reference Ab Initio Molecular Dynamics with a Classical Pressure Reservoir: Simulation of Pressure-Induced Amorphization in a Si35H36 Cluster
We present a new constant-pressure ab initio molecular dynamics method suitable for studying, e.g., pressure-induced structural transformations in finite nonperiodic systems such as clusters. We immerse an ab initio treated cluster into a model classical liquid, described by a soft-sphere potential, which acts as a pressure reservoir. The pressure is varied by tuning the parameter of the liquid potential. We apply the method to a Si35H36 cluster, which undergoes a pressure-induced amorphization at ∼35GPa, and remains in a disordered state even upon pressure release.
Article Reference Ab initio Simulation of Phase Transitions and Dissociation of H2S at High Pressure
By ab initio constant pressure molecular dynamics, we have identified the structure of phase V and phase VI of H2S at 35 and 65 GPa, respectively. The theoretical IR spectra of both phases are consistent with experimental findings and support our proposed structural models. We find that phase V is characterized by the presence of charged SH3+ and SH- species which are created and destroyed dynamically, whereas phase VI is no longer a molecular phase but consists of sheets of S with the majority of H intercalated between the layers. The stability of the two phases with respect to dissociation into elemental crystalline hydrogen and sulfur is discussed.
Inbook Reference Ab-initio Molecular Dynamics: Theory and Implementation
 
Article Reference All-electron ab-initio molecular dynamics
We present an all-electron implementation of the Gaussian and augmented plane wave density functional method (GAPW method), which allows ab-initio density functional calculations for periodic and non-periodic systems. The GAPW method uses a Gaussian basis set to expand the Kohn-Sham orbitals, whereas an augmented plane wave basis set is introduced as an auxiliary basis set to expand the electronic charge density. The results of the all-electron calculations for a representative set of small molecules are reported to demonstrate the accuracy and reliability of the GAPW method. Furthermore, its performance is shown for some larger systems, including calculations on unbranched alkane chains up to n-C100H202 with 1804 basis functions and a fully hydrated crystalline RNA duplex (sodium guanylyl-3[prime or minute]-5[prime or minute]-cytidine nonahydrate) with 368 atoms and 3168 basis functions. Finally, as a first test an all-electron ab-initio molecular dynamics (MD) run was performed for 32 water molecules in a simple cubic box under ambient conditions. A standard single processor workstation (IBM 397) was used for all the presented calculations.
Article Reference Aspects of hybrid QM/MM calculations: The treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase
 
Article Reference Car-Parrinello Simulation of Water at Supercritical Conditions
We present a first principles molecular dynamics study of water at the supercritical conditions T=647 K and ρ=0.322 g/cm3. At these conditions, the H-bonds are continuously broken and reformed in a dynamical fashion. We analyze the peculiar H-bond environment in terms of molecular configurations and dipole moment distribution. The latter shows that on average about half of the molecules still keep their gas phase character, not forming any H-bond, while the others cluster mostly in dimer and trimer configurations.
Article Reference Catalytic Reactions of Living Polymers: Density Functional Study of Reactivity of Phenol and Phenoxides with the Cyclic Tetramer of Polycarbonate
The reactivity of phenol, lithium phenoxide (LiOPh), and sodium phenoxide (NaOPh) with the cyclic tetramer of bisphenol A polycarbonate (BPA-PC) has been investigated using density functional calculations. The potential energy of the system is computed using a suitable reaction coordinate and relaxing all other degrees of freedom by CarParrinello molecular dynamics. Both LiOPh and NaOPh catalyze ring opening with small energy barriers (DeltaE = 4.0, 2.5 kcal/mol, respectively) to a chain with a phenyl carbonate at one end and a phenoxide at the other, a living polymer. The barrier is large for phenol (DeltaE 40 kcal/mol), but the total energy differences between the reactants and the chain are very small in all three molecules. We discuss the balance between changes in entropy and energy, and we compute the vibrational properties of metastable intermediate species.
Article Reference Cation-π versus OH-π Interactions in Proteins: A Density Functional Study
Structure and bonding of a cation-pi complex and an OH-pi adduct are investigated using density functional theory with gradient-corrections for the exchange-correlation functional. Our calculations are carried out for two specific model complexes representing (i) the thymine/Arg 72 adduct in the ternary complex of HIV-1 reverse transcriptase (RT) with a DNA template primer and a deoxynucleoside triphosphate (Huang, H., et al. Science 1998, 282, 16691675) and (ii) the Tyr6-Thr13 adduct in mu-gluthatione transferase (mu-GST) (Xiao, G., et al. Biochemistry 1996, 35, 47534765). We find that electrostatic interactions play an important role and provide similar stabilization energies to the two pi complexes. In HIV-1 RT, the pi electronic density of thymine is essentially uneffected by the presence of the arginine guanidium group; on the contrary, tyrosine is significantly polarized by the interaction with the hydroxyl group and other groups present in the mu-GST enzyme. The influence of Thr13 induced-polarization on Tyr6 pKa is compared with that of other interacting groups at the active site.
Article Reference Charge carrier interactions in ionic conductors: A classical molecular-dynamics and Monte Carlo study on AgI
 
Article Reference Chiral Palladium(II)−Bis(trichlorosilyl) Complexes. Synthesis, Structure, and Combined QM/MM Computational Studies
QM/MM computational studies have provided a detailed picture for the anomalous structural characteristics of the non-square-planar palladium(II) bis(trichlorosilyl) complex 6. The compound is relevant to catalytic asymmetric hydrosilylation and features the longest PdP bond ever observed of 2.503(2) A, as determined by X-ray crystallography.
Article Reference Clathrates as effective p-type and n-type tetrahedral carbon semiconductors
Based on ab initio calculations, we predict that a carbon clathrate compound (hexagonal C40) is suitable to be n doped by Li insertion and p doped by substitutional boron. This material represents an example of n- and p-type tetrahedral carbon semiconductor, alternative to the n-doped diamondlike films whose realization is still in progress. Although this compound has not been synthesized so far, its study can also provide insights into the properties of nanostructured carbon thin films, grown by supersonic cluster beam deposition techniques that display local morphologies similar to the channels and fullereniclike cages present in the system here investigated.
Article Reference Compton Anisotropy from Wannier Functions in the Case of Ice Ih
 
Article Reference Conformational Equilibria of Peroxynitrous Acid in Water: A First-Principles Molecular Dynamics Study
An aqueous solution of peroxynitrous acid has been studied using first-principles molecular dynamics simulations based on density functional theory. The relative Helmholtz energies of different conformers have been determined via thermodynamic integration with constraints. At contrast to the gas phase, only two conformers, a cis and a trans isomer, are present in solution and their relative Helmholtz energy is enhanced with respect to the gas phase. The average structural properties of the two conformational forms on the other hand are very close to the respective gas phase values. The interconversion pathway between the two conformers has been determined, and the Helmholtz energy profile for the isomerization reaction in solution is presented. The rotational barrier is calculated to be substantially higher than in gas phase due to a strong rearrangement of the solvent during the reaction. The structure of the transition state can only be described correctly when the solvent is taken explicitly into account. Our calculations indicate that the cis form is the dominant species in aqueous solution at ambient temperatures.
Article Reference Conformational flexibility of the catalytic Asp dyad in HIV-1 protease: An ab initio study on the free enzyme
 
Article Reference Density Functional Study of 17O NMR Chemical Shift and Nuclear Quadrupole Coupling Tensors in Oxyheme Model Complexes
The 17O NMR chemical shift tensors for a dioxygen ligand bound to iron porphyrin model complexes, with or without inclusion of picket-fence-type substituents, have been calculated by density functional IGLO approaches, based on structures optimized in CarParrinello molecular dynamics simulations. The calculations confirm the experimentally found, extremely large 17O shifts, and the assignment of the higher-frequency signal to the terminal oxygen position. Metalligand pi-back-bonding and the presence of low-lying excited states influence the chemical shift tensors characteristically. The magnitude and orientation of the shift tensors also reflect the close analogy to the bonding in the ozone molecule. Possible explanations for the temperature dependence of the solid-state NMR spectra are discussed. The computed 17O nuclear quadrupole coupling constants of ca. 11 MHz and ca. 17 MHz for bridging and terminal oxygen positions are close to the results for ozone, where theory and experiment agree well. This contradicts earlier assumptions of very small 17O field gradients for picket-fence oxyheme models and raises some questions about the analysis of the solid-state 17O NMR spectra. Possible reasons for the temperature dependence of the line widths in the solution spectra are suggested. We also discuss the implications of the 17O NMR spectra for the nature of the ground state of oxyheme complexes.
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